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Designing a More Accurate Protein Census

Graphic: Leza BerardoneApplied Biosystems will soon begin testing new mass spectrometry machines designed to identify proteins in as many as 1,000 samples per hour. For the machines to work as planned, however, each sample must be prefractionated down to just a handful of proteins, according to Stephen A. Martin, director of the company's proteomics research center in Framingham, Mass. This example suggests how the slower protocols leading to mass spec are as important to the progress of proteom

Douglas Steinberg
Graphic: Leza Berardone
Applied Biosystems will soon begin testing new mass spectrometry machines designed to identify proteins in as many as 1,000 samples per hour. For the machines to work as planned, however, each sample must be prefractionated down to just a handful of proteins, according to Stephen A. Martin, director of the company's proteomics research center in Framingham, Mass. This example suggests how the slower protocols leading to mass spec are as important to the progress of proteomics as are mass spec's higher-throughput capabilities.

These protocols have a serious limitation. Just as the Census Bureau's methods lead to the undercounting of certain population groups, the protocols lead researchers to under-identify whole classes of proteins. But clever strategies to attack this problem are starting to appear. Two papers published this month unveil chemistry-based methods that help recognize phosphorylated proteins.1,2 And a paper published last month presented a process...

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